Multiple sequence alignment - TraesCS6A01G358000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G358000 chr6A 100.000 4592 0 0 1 4592 587972807 587968216 0.000000e+00 8480.0
1 TraesCS6A01G358000 chr6A 89.276 3068 240 35 627 3639 587890288 587893321 0.000000e+00 3760.0
2 TraesCS6A01G358000 chr6A 80.391 1688 237 47 643 2288 775007 773372 0.000000e+00 1197.0
3 TraesCS6A01G358000 chr6A 90.619 533 33 2 4017 4541 587893739 587894262 0.000000e+00 691.0
4 TraesCS6A01G358000 chr6A 82.143 336 43 10 4267 4590 587894241 587894571 5.850000e-69 272.0
5 TraesCS6A01G358000 chr6A 90.000 170 10 7 53 218 505025792 505025626 3.600000e-51 213.0
6 TraesCS6A01G358000 chr6A 90.278 144 12 2 76 218 54940880 54940738 2.180000e-43 187.0
7 TraesCS6A01G358000 chr6A 97.500 40 1 0 589 628 587890087 587890126 8.240000e-08 69.4
8 TraesCS6A01G358000 chr6D 92.772 3611 178 21 219 3771 439662924 439659339 0.000000e+00 5145.0
9 TraesCS6A01G358000 chr6D 91.931 2268 137 17 627 2862 439616051 439618304 0.000000e+00 3133.0
10 TraesCS6A01G358000 chr6D 79.783 2577 376 75 643 3156 2133977 2136471 0.000000e+00 1738.0
11 TraesCS6A01G358000 chr6D 91.297 632 37 12 3963 4590 439656835 439656218 0.000000e+00 846.0
12 TraesCS6A01G358000 chr6D 83.026 760 102 12 2904 3642 439618384 439619137 0.000000e+00 664.0
13 TraesCS6A01G358000 chr6D 86.031 587 58 12 4017 4592 439619502 439620075 3.930000e-170 608.0
14 TraesCS6A01G358000 chr6D 79.369 761 99 31 1540 2288 4209039 4209753 2.480000e-132 483.0
15 TraesCS6A01G358000 chr6D 91.447 152 11 2 68 218 291937844 291937694 1.670000e-49 207.0
16 TraesCS6A01G358000 chr6B 92.834 2428 96 28 2171 4592 664523577 664521222 0.000000e+00 3448.0
17 TraesCS6A01G358000 chr6B 92.095 2024 117 13 628 2620 664477306 664479317 0.000000e+00 2811.0
18 TraesCS6A01G358000 chr6B 91.924 1944 95 21 219 2132 664525581 664523670 0.000000e+00 2663.0
19 TraesCS6A01G358000 chr6B 79.745 2197 334 61 643 2782 3799634 3801776 0.000000e+00 1489.0
20 TraesCS6A01G358000 chr6B 81.129 1187 159 38 2508 3642 664479316 664480489 0.000000e+00 891.0
21 TraesCS6A01G358000 chr6B 88.560 507 42 7 4019 4518 664501719 664501222 6.570000e-168 601.0
22 TraesCS6A01G358000 chr6B 96.429 84 3 0 975 1058 664507920 664508003 6.200000e-29 139.0
23 TraesCS6A01G358000 chr6B 93.827 81 5 0 4512 4592 664501032 664500952 6.240000e-24 122.0
24 TraesCS6A01G358000 chr6B 96.154 52 2 0 2118 2169 664523656 664523605 8.190000e-13 86.1
25 TraesCS6A01G358000 chr2D 92.667 150 8 3 71 218 109551662 109551810 3.600000e-51 213.0
26 TraesCS6A01G358000 chr2D 100.000 29 0 0 3869 3897 10825665 10825693 2.000000e-03 54.7
27 TraesCS6A01G358000 chr4D 91.096 146 11 2 75 219 73214905 73214761 3.620000e-46 196.0
28 TraesCS6A01G358000 chr4D 91.034 145 11 2 75 218 73216493 73216350 1.300000e-45 195.0
29 TraesCS6A01G358000 chr4D 96.970 33 0 1 3869 3901 414149783 414149752 2.000000e-03 54.7
30 TraesCS6A01G358000 chr7D 88.667 150 16 1 70 218 7703594 7703743 1.010000e-41 182.0
31 TraesCS6A01G358000 chr2A 85.876 177 11 11 52 218 573659411 573659239 4.720000e-40 176.0
32 TraesCS6A01G358000 chr1A 85.714 175 14 10 52 218 12821983 12821812 1.700000e-39 174.0
33 TraesCS6A01G358000 chr1D 100.000 53 0 0 1 53 478158632 478158684 1.050000e-16 99.0
34 TraesCS6A01G358000 chr1D 100.000 51 0 0 1 51 38562921 38562971 1.360000e-15 95.3
35 TraesCS6A01G358000 chr7B 100.000 52 0 0 1 52 484271288 484271237 3.780000e-16 97.1
36 TraesCS6A01G358000 chr7B 96.875 32 1 0 3869 3900 497083882 497083913 2.000000e-03 54.7
37 TraesCS6A01G358000 chrUn 100.000 51 0 0 1 51 155863 155913 1.360000e-15 95.3
38 TraesCS6A01G358000 chrUn 100.000 51 0 0 1 51 29208109 29208159 1.360000e-15 95.3
39 TraesCS6A01G358000 chrUn 100.000 51 0 0 1 51 31367852 31367902 1.360000e-15 95.3
40 TraesCS6A01G358000 chrUn 100.000 51 0 0 1 51 33368616 33368566 1.360000e-15 95.3
41 TraesCS6A01G358000 chrUn 100.000 51 0 0 1 51 200950350 200950400 1.360000e-15 95.3
42 TraesCS6A01G358000 chrUn 100.000 51 0 0 1 51 404649419 404649469 1.360000e-15 95.3
43 TraesCS6A01G358000 chr7A 94.595 37 1 1 3869 3905 478025088 478025053 6.420000e-04 56.5
44 TraesCS6A01G358000 chr4B 96.970 33 1 0 3869 3901 172205890 172205858 6.420000e-04 56.5
45 TraesCS6A01G358000 chr2B 97.059 34 0 1 3869 3901 690942962 690942995 6.420000e-04 56.5
46 TraesCS6A01G358000 chr5D 100.000 29 0 0 3869 3897 513352434 513352406 2.000000e-03 54.7
47 TraesCS6A01G358000 chr3B 96.875 32 1 0 3869 3900 778238119 778238150 2.000000e-03 54.7
48 TraesCS6A01G358000 chr4A 94.286 35 1 1 3869 3902 32650588 32650622 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G358000 chr6A 587968216 587972807 4591 True 8480.000000 8480 100.000000 1 4592 1 chr6A.!!$R4 4591
1 TraesCS6A01G358000 chr6A 587890087 587894571 4484 False 1198.100000 3760 89.884500 589 4590 4 chr6A.!!$F1 4001
2 TraesCS6A01G358000 chr6A 773372 775007 1635 True 1197.000000 1197 80.391000 643 2288 1 chr6A.!!$R1 1645
3 TraesCS6A01G358000 chr6D 439656218 439662924 6706 True 2995.500000 5145 92.034500 219 4590 2 chr6D.!!$R2 4371
4 TraesCS6A01G358000 chr6D 2133977 2136471 2494 False 1738.000000 1738 79.783000 643 3156 1 chr6D.!!$F1 2513
5 TraesCS6A01G358000 chr6D 439616051 439620075 4024 False 1468.333333 3133 86.996000 627 4592 3 chr6D.!!$F3 3965
6 TraesCS6A01G358000 chr6D 4209039 4209753 714 False 483.000000 483 79.369000 1540 2288 1 chr6D.!!$F2 748
7 TraesCS6A01G358000 chr6B 664521222 664525581 4359 True 2065.700000 3448 93.637333 219 4592 3 chr6B.!!$R2 4373
8 TraesCS6A01G358000 chr6B 664477306 664480489 3183 False 1851.000000 2811 86.612000 628 3642 2 chr6B.!!$F3 3014
9 TraesCS6A01G358000 chr6B 3799634 3801776 2142 False 1489.000000 1489 79.745000 643 2782 1 chr6B.!!$F1 2139
10 TraesCS6A01G358000 chr6B 664500952 664501719 767 True 361.500000 601 91.193500 4019 4592 2 chr6B.!!$R1 573

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
31 32 0.168788 CGCCTACGGTGACTTCGTAA 59.831 55.000 0.0 0.00 41.62 3.18 F
32 33 1.401409 CGCCTACGGTGACTTCGTAAA 60.401 52.381 0.0 0.00 41.62 2.01 F
1286 1483 1.671556 CGGCTTTTAACCACCCATTGC 60.672 52.381 0.0 0.00 0.00 3.56 F
2523 2837 0.465460 TGGGATTGGCGCCTTACATC 60.465 55.000 29.7 21.28 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2226 3.694566 ACCCTCGATGGAAAATTAACTGC 59.305 43.478 14.21 0.0 38.35 4.40 R
2185 2477 9.345517 CCTTCATGTACAACTGAAATAATGTTG 57.654 33.333 11.89 0.0 44.44 3.33 R
3370 3872 0.179018 AAATGCCCGCTACCCATCTC 60.179 55.000 0.00 0.0 0.00 2.75 R
3854 6216 1.204941 AGTCCGCCACAAGTACAGATC 59.795 52.381 0.00 0.0 0.00 2.75 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.883300 GACGACGAGGCGCCTACG 62.883 72.222 32.91 32.91 44.07 3.51
22 23 4.849329 GACGAGGCGCCTACGGTG 62.849 72.222 34.97 23.88 40.57 4.94
24 25 4.849329 CGAGGCGCCTACGGTGAC 62.849 72.222 32.97 14.51 42.50 3.67
27 28 2.508663 GGCGCCTACGGTGACTTC 60.509 66.667 22.15 0.00 38.38 3.01
28 29 2.879462 GCGCCTACGGTGACTTCG 60.879 66.667 0.00 0.00 40.57 3.79
29 30 2.564975 CGCCTACGGTGACTTCGT 59.435 61.111 0.00 0.00 43.64 3.85
30 31 1.796151 CGCCTACGGTGACTTCGTA 59.204 57.895 0.00 0.00 41.38 3.43
31 32 0.168788 CGCCTACGGTGACTTCGTAA 59.831 55.000 0.00 0.00 41.62 3.18
32 33 1.401409 CGCCTACGGTGACTTCGTAAA 60.401 52.381 0.00 0.00 41.62 2.01
33 34 2.733227 CGCCTACGGTGACTTCGTAAAT 60.733 50.000 0.00 0.00 41.62 1.40
34 35 2.856557 GCCTACGGTGACTTCGTAAATC 59.143 50.000 0.00 0.00 41.62 2.17
35 36 3.428589 GCCTACGGTGACTTCGTAAATCT 60.429 47.826 0.00 0.00 41.62 2.40
36 37 4.349501 CCTACGGTGACTTCGTAAATCTC 58.650 47.826 0.00 0.00 41.62 2.75
37 38 3.928727 ACGGTGACTTCGTAAATCTCA 57.071 42.857 0.00 0.00 39.22 3.27
38 39 4.247267 ACGGTGACTTCGTAAATCTCAA 57.753 40.909 0.00 0.00 39.22 3.02
39 40 4.235360 ACGGTGACTTCGTAAATCTCAAG 58.765 43.478 0.00 0.00 39.22 3.02
40 41 4.022589 ACGGTGACTTCGTAAATCTCAAGA 60.023 41.667 0.00 0.00 39.22 3.02
41 42 5.103000 CGGTGACTTCGTAAATCTCAAGAT 58.897 41.667 0.00 0.00 36.07 2.40
42 43 5.004821 CGGTGACTTCGTAAATCTCAAGATG 59.995 44.000 0.00 0.00 34.49 2.90
43 44 6.100004 GGTGACTTCGTAAATCTCAAGATGA 58.900 40.000 0.00 0.00 34.49 2.92
44 45 6.758886 GGTGACTTCGTAAATCTCAAGATGAT 59.241 38.462 0.00 0.00 34.49 2.45
45 46 7.921214 GGTGACTTCGTAAATCTCAAGATGATA 59.079 37.037 0.00 0.00 34.49 2.15
46 47 9.469807 GTGACTTCGTAAATCTCAAGATGATAT 57.530 33.333 0.00 0.00 34.49 1.63
47 48 9.468532 TGACTTCGTAAATCTCAAGATGATATG 57.531 33.333 0.00 0.00 34.49 1.78
48 49 8.304202 ACTTCGTAAATCTCAAGATGATATGC 57.696 34.615 0.00 0.00 34.49 3.14
49 50 7.386299 ACTTCGTAAATCTCAAGATGATATGCC 59.614 37.037 0.00 0.00 34.49 4.40
50 51 5.863935 TCGTAAATCTCAAGATGATATGCCG 59.136 40.000 0.00 0.00 34.49 5.69
51 52 5.635280 CGTAAATCTCAAGATGATATGCCGT 59.365 40.000 0.00 0.00 34.49 5.68
52 53 6.146184 CGTAAATCTCAAGATGATATGCCGTT 59.854 38.462 0.00 0.00 34.49 4.44
53 54 5.936686 AATCTCAAGATGATATGCCGTTG 57.063 39.130 0.00 0.00 34.49 4.10
54 55 4.406648 TCTCAAGATGATATGCCGTTGT 57.593 40.909 0.00 0.00 0.00 3.32
55 56 5.529581 TCTCAAGATGATATGCCGTTGTA 57.470 39.130 0.00 0.00 0.00 2.41
56 57 5.532557 TCTCAAGATGATATGCCGTTGTAG 58.467 41.667 0.00 0.00 0.00 2.74
57 58 4.631131 TCAAGATGATATGCCGTTGTAGG 58.369 43.478 0.00 0.00 0.00 3.18
58 59 4.343814 TCAAGATGATATGCCGTTGTAGGA 59.656 41.667 0.00 0.00 0.00 2.94
59 60 5.012046 TCAAGATGATATGCCGTTGTAGGAT 59.988 40.000 0.00 0.00 0.00 3.24
60 61 4.825422 AGATGATATGCCGTTGTAGGATG 58.175 43.478 0.00 0.00 0.00 3.51
61 62 4.528206 AGATGATATGCCGTTGTAGGATGA 59.472 41.667 0.00 0.00 0.00 2.92
62 63 4.890158 TGATATGCCGTTGTAGGATGAT 57.110 40.909 0.00 0.00 0.00 2.45
63 64 5.227569 TGATATGCCGTTGTAGGATGATT 57.772 39.130 0.00 0.00 0.00 2.57
64 65 4.996758 TGATATGCCGTTGTAGGATGATTG 59.003 41.667 0.00 0.00 0.00 2.67
65 66 3.558931 ATGCCGTTGTAGGATGATTGA 57.441 42.857 0.00 0.00 0.00 2.57
66 67 3.342377 TGCCGTTGTAGGATGATTGAA 57.658 42.857 0.00 0.00 0.00 2.69
67 68 3.884895 TGCCGTTGTAGGATGATTGAAT 58.115 40.909 0.00 0.00 0.00 2.57
68 69 5.029807 TGCCGTTGTAGGATGATTGAATA 57.970 39.130 0.00 0.00 0.00 1.75
69 70 5.620206 TGCCGTTGTAGGATGATTGAATAT 58.380 37.500 0.00 0.00 0.00 1.28
70 71 6.061441 TGCCGTTGTAGGATGATTGAATATT 58.939 36.000 0.00 0.00 0.00 1.28
71 72 6.017192 TGCCGTTGTAGGATGATTGAATATTG 60.017 38.462 0.00 0.00 0.00 1.90
72 73 6.017109 GCCGTTGTAGGATGATTGAATATTGT 60.017 38.462 0.00 0.00 0.00 2.71
73 74 7.355017 CCGTTGTAGGATGATTGAATATTGTG 58.645 38.462 0.00 0.00 0.00 3.33
74 75 7.012327 CCGTTGTAGGATGATTGAATATTGTGT 59.988 37.037 0.00 0.00 0.00 3.72
75 76 8.397906 CGTTGTAGGATGATTGAATATTGTGTT 58.602 33.333 0.00 0.00 0.00 3.32
76 77 9.507280 GTTGTAGGATGATTGAATATTGTGTTG 57.493 33.333 0.00 0.00 0.00 3.33
77 78 8.806429 TGTAGGATGATTGAATATTGTGTTGT 57.194 30.769 0.00 0.00 0.00 3.32
78 79 9.898152 TGTAGGATGATTGAATATTGTGTTGTA 57.102 29.630 0.00 0.00 0.00 2.41
89 90 8.892723 TGAATATTGTGTTGTATTGATCTCACC 58.107 33.333 0.00 0.00 0.00 4.02
90 91 9.113838 GAATATTGTGTTGTATTGATCTCACCT 57.886 33.333 0.00 0.00 0.00 4.00
96 97 9.546428 TGTGTTGTATTGATCTCACCTAATATG 57.454 33.333 0.00 0.00 0.00 1.78
97 98 8.993121 GTGTTGTATTGATCTCACCTAATATGG 58.007 37.037 0.00 0.00 0.00 2.74
98 99 8.156820 TGTTGTATTGATCTCACCTAATATGGG 58.843 37.037 0.00 0.00 0.00 4.00
99 100 7.257790 TGTATTGATCTCACCTAATATGGGG 57.742 40.000 0.00 0.00 0.00 4.96
100 101 6.792473 TGTATTGATCTCACCTAATATGGGGT 59.208 38.462 0.00 0.00 36.07 4.95
101 102 7.959152 TGTATTGATCTCACCTAATATGGGGTA 59.041 37.037 0.00 0.00 34.07 3.69
102 103 8.993424 GTATTGATCTCACCTAATATGGGGTAT 58.007 37.037 0.00 0.00 34.07 2.73
104 105 9.749996 ATTGATCTCACCTAATATGGGGTATAT 57.250 33.333 0.00 0.00 34.07 0.86
121 122 9.883293 TGGGGTATATATAGAATACATGAGAGG 57.117 37.037 0.00 0.00 32.49 3.69
129 130 7.896383 ATAGAATACATGAGAGGATAGAGGC 57.104 40.000 0.00 0.00 0.00 4.70
130 131 5.902760 AGAATACATGAGAGGATAGAGGCT 58.097 41.667 0.00 0.00 0.00 4.58
131 132 6.322126 AGAATACATGAGAGGATAGAGGCTT 58.678 40.000 0.00 0.00 0.00 4.35
132 133 5.999205 ATACATGAGAGGATAGAGGCTTG 57.001 43.478 0.00 0.00 0.00 4.01
133 134 3.921104 ACATGAGAGGATAGAGGCTTGA 58.079 45.455 0.00 0.00 0.00 3.02
134 135 4.293494 ACATGAGAGGATAGAGGCTTGAA 58.707 43.478 0.00 0.00 0.00 2.69
135 136 4.344679 ACATGAGAGGATAGAGGCTTGAAG 59.655 45.833 0.00 0.00 0.00 3.02
136 137 3.987745 TGAGAGGATAGAGGCTTGAAGT 58.012 45.455 0.00 0.00 0.00 3.01
137 138 5.130705 TGAGAGGATAGAGGCTTGAAGTA 57.869 43.478 0.00 0.00 0.00 2.24
138 139 4.890581 TGAGAGGATAGAGGCTTGAAGTAC 59.109 45.833 0.00 0.00 0.00 2.73
139 140 4.873010 AGAGGATAGAGGCTTGAAGTACA 58.127 43.478 0.00 0.00 0.00 2.90
140 141 5.273208 AGAGGATAGAGGCTTGAAGTACAA 58.727 41.667 0.00 0.00 36.97 2.41
156 157 8.771920 TGAAGTACAAGACAAGTAATACATGG 57.228 34.615 0.00 0.00 0.00 3.66
157 158 8.372459 TGAAGTACAAGACAAGTAATACATGGT 58.628 33.333 0.00 0.00 0.00 3.55
158 159 9.216117 GAAGTACAAGACAAGTAATACATGGTT 57.784 33.333 0.00 0.00 0.00 3.67
159 160 9.569122 AAGTACAAGACAAGTAATACATGGTTT 57.431 29.630 0.00 0.00 0.00 3.27
180 181 8.890124 GGTTTAAACCTATTCCATCTCTACTC 57.110 38.462 26.98 0.00 45.75 2.59
181 182 7.932491 GGTTTAAACCTATTCCATCTCTACTCC 59.068 40.741 26.98 0.00 45.75 3.85
182 183 8.706521 GTTTAAACCTATTCCATCTCTACTCCT 58.293 37.037 7.12 0.00 0.00 3.69
183 184 8.855804 TTAAACCTATTCCATCTCTACTCCTT 57.144 34.615 0.00 0.00 0.00 3.36
184 185 9.947189 TTAAACCTATTCCATCTCTACTCCTTA 57.053 33.333 0.00 0.00 0.00 2.69
186 187 8.658840 AACCTATTCCATCTCTACTCCTTATC 57.341 38.462 0.00 0.00 0.00 1.75
187 188 8.006967 ACCTATTCCATCTCTACTCCTTATCT 57.993 38.462 0.00 0.00 0.00 1.98
188 189 8.113462 ACCTATTCCATCTCTACTCCTTATCTC 58.887 40.741 0.00 0.00 0.00 2.75
189 190 8.336235 CCTATTCCATCTCTACTCCTTATCTCT 58.664 40.741 0.00 0.00 0.00 3.10
436 438 4.039245 TGTTCCTAGTCTCTCACAACCAAG 59.961 45.833 0.00 0.00 0.00 3.61
455 458 6.838382 ACCAAGTTAAACTCACCTCATAACT 58.162 36.000 0.00 0.00 38.17 2.24
541 545 7.593825 AGCCGATGGTATAAAATATTTCAAGC 58.406 34.615 0.10 1.08 0.00 4.01
776 943 5.419542 TGTACAAAAGAGAAGGATCGATGG 58.580 41.667 0.54 0.00 0.00 3.51
1102 1299 2.708325 AGAAGGCAAGAGGAAGACAGTT 59.292 45.455 0.00 0.00 0.00 3.16
1286 1483 1.671556 CGGCTTTTAACCACCCATTGC 60.672 52.381 0.00 0.00 0.00 3.56
1302 1499 5.170748 CCCATTGCTGAAAGACCATAAAAC 58.829 41.667 0.00 0.00 34.07 2.43
1353 1550 3.728076 ATGCATCCATGAATTGCTCAC 57.272 42.857 13.28 0.00 36.69 3.51
1440 1639 7.283127 TGTTTCAGTAATCTTTCTGGATATGCC 59.717 37.037 0.00 0.00 33.13 4.40
1559 1775 8.400947 AGCATGTTTTGTATGTATTGTCTGATC 58.599 33.333 0.00 0.00 0.00 2.92
1750 1967 2.289565 GGAAGTAGCACCATAGCAACC 58.710 52.381 0.00 0.00 36.85 3.77
1783 2000 2.423185 TGGGCTCAAAAACGATATGCAG 59.577 45.455 0.00 0.00 0.00 4.41
2153 2418 4.178545 AGGAATGATTTTTGTGCCTTCG 57.821 40.909 0.00 0.00 0.00 3.79
2217 2509 7.815840 TTTCAGTTGTACATGAAGGAATTCA 57.184 32.000 7.93 0.00 36.81 2.57
2233 2525 9.927668 GAAGGAATTCAAATTTCATTACCAAGA 57.072 29.630 7.93 0.00 0.00 3.02
2344 2642 4.888326 TTCCTTCCCAAAATGTGAATGG 57.112 40.909 0.00 0.00 0.00 3.16
2523 2837 0.465460 TGGGATTGGCGCCTTACATC 60.465 55.000 29.70 21.28 0.00 3.06
2539 2853 8.757789 CGCCTTACATCTTTTATAACGTGAATA 58.242 33.333 0.00 0.00 0.00 1.75
2595 3020 8.071967 ACATAGTATTCATTCATCACATTTGCG 58.928 33.333 0.00 0.00 0.00 4.85
2598 3023 3.763097 TCATTCATCACATTTGCGGAC 57.237 42.857 0.00 0.00 0.00 4.79
2607 3032 2.970609 CACATTTGCGGACGTTACTTTG 59.029 45.455 0.00 0.00 0.00 2.77
2637 3062 1.797211 GAGGGCGGGACTCAGATACG 61.797 65.000 0.00 0.00 35.09 3.06
2746 3172 7.729881 TGGATAAATATTGAAAATGGAGGAGGG 59.270 37.037 0.00 0.00 0.00 4.30
2840 3275 3.687212 TCATGTTGCTTGGGTACGTAATG 59.313 43.478 0.00 0.00 0.00 1.90
2841 3276 1.807742 TGTTGCTTGGGTACGTAATGC 59.192 47.619 0.00 0.00 0.00 3.56
2842 3277 1.807742 GTTGCTTGGGTACGTAATGCA 59.192 47.619 0.00 0.00 0.00 3.96
2843 3278 2.411628 TGCTTGGGTACGTAATGCAT 57.588 45.000 0.00 0.00 0.00 3.96
2844 3279 3.545366 TGCTTGGGTACGTAATGCATA 57.455 42.857 0.00 0.00 0.00 3.14
2845 3280 3.199677 TGCTTGGGTACGTAATGCATAC 58.800 45.455 0.00 0.00 0.00 2.39
2846 3281 3.118555 TGCTTGGGTACGTAATGCATACT 60.119 43.478 0.00 0.00 31.96 2.12
2847 3282 4.099727 TGCTTGGGTACGTAATGCATACTA 59.900 41.667 0.00 0.00 31.96 1.82
2848 3283 5.221561 TGCTTGGGTACGTAATGCATACTAT 60.222 40.000 0.00 0.00 31.96 2.12
2849 3284 5.699458 GCTTGGGTACGTAATGCATACTATT 59.301 40.000 0.00 0.00 31.96 1.73
2850 3285 6.869913 GCTTGGGTACGTAATGCATACTATTA 59.130 38.462 0.00 0.00 31.96 0.98
2851 3286 7.548075 GCTTGGGTACGTAATGCATACTATTAT 59.452 37.037 0.00 0.00 31.96 1.28
2852 3287 9.431887 CTTGGGTACGTAATGCATACTATTATT 57.568 33.333 0.00 0.00 31.96 1.40
2853 3288 9.781633 TTGGGTACGTAATGCATACTATTATTT 57.218 29.630 0.00 0.00 31.96 1.40
2854 3289 9.210329 TGGGTACGTAATGCATACTATTATTTG 57.790 33.333 0.00 0.00 31.96 2.32
2855 3290 8.662141 GGGTACGTAATGCATACTATTATTTGG 58.338 37.037 0.00 0.00 31.96 3.28
2856 3291 9.426837 GGTACGTAATGCATACTATTATTTGGA 57.573 33.333 0.00 0.00 31.96 3.53
2888 3369 9.125026 ACAGGCTATTATTGGCTATATATTTGC 57.875 33.333 2.29 0.00 38.29 3.68
2965 3454 3.399330 ACAAACTTCACAGTACGATGGG 58.601 45.455 0.00 0.00 30.68 4.00
3010 3499 3.521126 ACTTCAGCTGTCCTGGATATGTT 59.479 43.478 14.67 0.00 42.05 2.71
3151 3652 4.143030 CGATTTCTCAAGCACCTTGTACAG 60.143 45.833 0.00 0.00 41.66 2.74
3314 3816 7.880160 TCAAATTCATTAGATACAAGGGTGG 57.120 36.000 0.00 0.00 0.00 4.61
3318 3820 8.664669 AATTCATTAGATACAAGGGTGGTTTT 57.335 30.769 0.00 0.00 0.00 2.43
3370 3872 2.464459 GCCGCATCAAACTCTCCGG 61.464 63.158 0.00 0.00 38.76 5.14
3395 3897 0.246360 GGTAGCGGGCATTTTGCTTT 59.754 50.000 0.00 0.00 44.28 3.51
3445 3947 3.514777 GGCATCGAGATTGCCGATA 57.485 52.632 12.49 0.00 43.93 2.92
3554 4056 8.548877 TGAAGTTAGAAAGGATTTAGGTATGCT 58.451 33.333 0.00 0.00 39.27 3.79
3556 4058 9.755122 AAGTTAGAAAGGATTTAGGTATGCTTT 57.245 29.630 3.28 3.28 45.24 3.51
3668 4187 2.031683 GTGGTCTTGCGGCATTATGTAC 59.968 50.000 2.28 0.00 0.00 2.90
3849 6211 4.625607 ACGGTCATCCTTCTTTCTTCTT 57.374 40.909 0.00 0.00 0.00 2.52
3854 6216 6.091441 CGGTCATCCTTCTTTCTTCTTAACAG 59.909 42.308 0.00 0.00 0.00 3.16
3858 6220 8.820831 TCATCCTTCTTTCTTCTTAACAGATCT 58.179 33.333 0.00 0.00 0.00 2.75
3859 6221 8.881743 CATCCTTCTTTCTTCTTAACAGATCTG 58.118 37.037 21.37 21.37 0.00 2.90
3861 6223 9.090103 TCCTTCTTTCTTCTTAACAGATCTGTA 57.910 33.333 28.10 13.18 44.13 2.74
3863 6225 9.921637 CTTCTTTCTTCTTAACAGATCTGTACT 57.078 33.333 28.10 16.32 44.13 2.73
3865 6227 9.698309 TCTTTCTTCTTAACAGATCTGTACTTG 57.302 33.333 28.10 17.54 44.13 3.16
3866 6228 9.482627 CTTTCTTCTTAACAGATCTGTACTTGT 57.517 33.333 28.10 14.85 44.13 3.16
3868 6230 7.378966 TCTTCTTAACAGATCTGTACTTGTGG 58.621 38.462 28.10 15.21 44.13 4.17
3869 6231 5.479306 TCTTAACAGATCTGTACTTGTGGC 58.521 41.667 28.10 0.00 44.13 5.01
3870 6232 2.370281 ACAGATCTGTACTTGTGGCG 57.630 50.000 26.87 0.00 42.90 5.69
3871 6233 1.066858 ACAGATCTGTACTTGTGGCGG 60.067 52.381 26.87 0.00 42.90 6.13
3872 6234 1.204704 CAGATCTGTACTTGTGGCGGA 59.795 52.381 14.95 0.00 0.00 5.54
3873 6235 1.204941 AGATCTGTACTTGTGGCGGAC 59.795 52.381 0.00 0.00 0.00 4.79
3874 6236 1.204941 GATCTGTACTTGTGGCGGACT 59.795 52.381 0.00 0.00 0.00 3.85
3875 6237 1.913778 TCTGTACTTGTGGCGGACTA 58.086 50.000 0.00 0.00 0.00 2.59
3876 6238 2.241160 TCTGTACTTGTGGCGGACTAA 58.759 47.619 0.00 0.00 0.00 2.24
3877 6239 2.629137 TCTGTACTTGTGGCGGACTAAA 59.371 45.455 0.00 0.00 0.00 1.85
3878 6240 3.069872 TCTGTACTTGTGGCGGACTAAAA 59.930 43.478 0.00 0.00 0.00 1.52
3879 6241 3.806380 TGTACTTGTGGCGGACTAAAAA 58.194 40.909 0.00 0.00 0.00 1.94
3880 6242 3.810941 TGTACTTGTGGCGGACTAAAAAG 59.189 43.478 0.00 0.00 0.00 2.27
3881 6243 3.202829 ACTTGTGGCGGACTAAAAAGA 57.797 42.857 0.00 0.00 0.00 2.52
3882 6244 3.547746 ACTTGTGGCGGACTAAAAAGAA 58.452 40.909 0.00 0.00 0.00 2.52
3883 6245 3.949113 ACTTGTGGCGGACTAAAAAGAAA 59.051 39.130 0.00 0.00 0.00 2.52
3884 6246 3.974871 TGTGGCGGACTAAAAAGAAAC 57.025 42.857 0.00 0.00 0.00 2.78
3885 6247 2.288458 TGTGGCGGACTAAAAAGAAACG 59.712 45.455 0.00 0.00 0.00 3.60
3886 6248 1.874872 TGGCGGACTAAAAAGAAACGG 59.125 47.619 0.00 0.00 0.00 4.44
3887 6249 2.145536 GGCGGACTAAAAAGAAACGGA 58.854 47.619 0.00 0.00 0.00 4.69
3888 6250 2.159037 GGCGGACTAAAAAGAAACGGAG 59.841 50.000 0.00 0.00 0.00 4.63
3889 6251 2.159037 GCGGACTAAAAAGAAACGGAGG 59.841 50.000 0.00 0.00 0.00 4.30
3890 6252 2.740447 CGGACTAAAAAGAAACGGAGGG 59.260 50.000 0.00 0.00 0.00 4.30
3891 6253 3.555586 CGGACTAAAAAGAAACGGAGGGA 60.556 47.826 0.00 0.00 0.00 4.20
3892 6254 4.001652 GGACTAAAAAGAAACGGAGGGAG 58.998 47.826 0.00 0.00 0.00 4.30
3938 7003 4.616604 CGGTCAACTCATTACTCGTTGGTA 60.617 45.833 0.00 0.00 38.74 3.25
3939 7004 4.863131 GGTCAACTCATTACTCGTTGGTAG 59.137 45.833 0.00 0.00 38.74 3.18
3942 7007 6.746364 GTCAACTCATTACTCGTTGGTAGTAG 59.254 42.308 0.00 0.00 38.74 2.57
3943 7008 5.246145 ACTCATTACTCGTTGGTAGTAGC 57.754 43.478 0.00 0.00 31.37 3.58
3945 7010 6.118170 ACTCATTACTCGTTGGTAGTAGCTA 58.882 40.000 0.35 0.00 31.37 3.32
3947 7012 6.967135 TCATTACTCGTTGGTAGTAGCTATG 58.033 40.000 0.00 0.00 31.37 2.23
3948 7013 5.762825 TTACTCGTTGGTAGTAGCTATGG 57.237 43.478 0.00 0.00 31.37 2.74
3949 7014 3.629087 ACTCGTTGGTAGTAGCTATGGT 58.371 45.455 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.883300 GTAGGCGCCTCGTCGTCG 62.883 72.222 36.73 0.00 39.34 5.12
2 3 4.883300 CGTAGGCGCCTCGTCGTC 62.883 72.222 36.73 15.88 36.23 4.20
15 16 4.978186 TGAGATTTACGAAGTCACCGTAG 58.022 43.478 0.00 0.00 43.93 3.51
16 17 5.181811 TCTTGAGATTTACGAAGTCACCGTA 59.818 40.000 0.00 0.00 43.93 4.02
17 18 3.928727 TGAGATTTACGAAGTCACCGT 57.071 42.857 0.00 0.00 43.93 4.83
18 19 4.482386 TCTTGAGATTTACGAAGTCACCG 58.518 43.478 0.00 0.00 43.93 4.94
19 20 6.100004 TCATCTTGAGATTTACGAAGTCACC 58.900 40.000 0.00 0.00 35.39 4.02
20 21 7.763172 ATCATCTTGAGATTTACGAAGTCAC 57.237 36.000 0.00 0.00 35.39 3.67
21 22 9.468532 CATATCATCTTGAGATTTACGAAGTCA 57.531 33.333 0.00 0.00 35.39 3.41
22 23 8.431593 GCATATCATCTTGAGATTTACGAAGTC 58.568 37.037 0.00 0.00 35.39 3.01
23 24 7.386299 GGCATATCATCTTGAGATTTACGAAGT 59.614 37.037 0.00 0.00 37.29 3.01
24 25 7.411264 CGGCATATCATCTTGAGATTTACGAAG 60.411 40.741 0.00 0.00 31.21 3.79
25 26 6.366061 CGGCATATCATCTTGAGATTTACGAA 59.634 38.462 0.00 0.00 31.21 3.85
26 27 5.863935 CGGCATATCATCTTGAGATTTACGA 59.136 40.000 0.00 0.00 31.21 3.43
27 28 5.635280 ACGGCATATCATCTTGAGATTTACG 59.365 40.000 0.00 0.00 31.21 3.18
28 29 7.041780 ACAACGGCATATCATCTTGAGATTTAC 60.042 37.037 0.00 0.00 31.21 2.01
29 30 6.992123 ACAACGGCATATCATCTTGAGATTTA 59.008 34.615 0.00 0.00 31.21 1.40
30 31 5.824624 ACAACGGCATATCATCTTGAGATTT 59.175 36.000 0.00 0.00 31.21 2.17
31 32 5.371526 ACAACGGCATATCATCTTGAGATT 58.628 37.500 0.00 0.00 31.21 2.40
32 33 4.965814 ACAACGGCATATCATCTTGAGAT 58.034 39.130 0.00 0.00 34.56 2.75
33 34 4.406648 ACAACGGCATATCATCTTGAGA 57.593 40.909 0.00 0.00 0.00 3.27
34 35 4.687948 CCTACAACGGCATATCATCTTGAG 59.312 45.833 0.00 0.00 0.00 3.02
35 36 4.343814 TCCTACAACGGCATATCATCTTGA 59.656 41.667 0.00 0.00 0.00 3.02
36 37 4.631131 TCCTACAACGGCATATCATCTTG 58.369 43.478 0.00 0.00 0.00 3.02
37 38 4.955811 TCCTACAACGGCATATCATCTT 57.044 40.909 0.00 0.00 0.00 2.40
38 39 4.528206 TCATCCTACAACGGCATATCATCT 59.472 41.667 0.00 0.00 0.00 2.90
39 40 4.820897 TCATCCTACAACGGCATATCATC 58.179 43.478 0.00 0.00 0.00 2.92
40 41 4.890158 TCATCCTACAACGGCATATCAT 57.110 40.909 0.00 0.00 0.00 2.45
41 42 4.890158 ATCATCCTACAACGGCATATCA 57.110 40.909 0.00 0.00 0.00 2.15
42 43 5.237815 TCAATCATCCTACAACGGCATATC 58.762 41.667 0.00 0.00 0.00 1.63
43 44 5.227569 TCAATCATCCTACAACGGCATAT 57.772 39.130 0.00 0.00 0.00 1.78
44 45 4.681074 TCAATCATCCTACAACGGCATA 57.319 40.909 0.00 0.00 0.00 3.14
45 46 3.558931 TCAATCATCCTACAACGGCAT 57.441 42.857 0.00 0.00 0.00 4.40
46 47 3.342377 TTCAATCATCCTACAACGGCA 57.658 42.857 0.00 0.00 0.00 5.69
47 48 6.017109 ACAATATTCAATCATCCTACAACGGC 60.017 38.462 0.00 0.00 0.00 5.68
48 49 7.012327 ACACAATATTCAATCATCCTACAACGG 59.988 37.037 0.00 0.00 0.00 4.44
49 50 7.919690 ACACAATATTCAATCATCCTACAACG 58.080 34.615 0.00 0.00 0.00 4.10
50 51 9.507280 CAACACAATATTCAATCATCCTACAAC 57.493 33.333 0.00 0.00 0.00 3.32
51 52 9.241919 ACAACACAATATTCAATCATCCTACAA 57.758 29.630 0.00 0.00 0.00 2.41
52 53 8.806429 ACAACACAATATTCAATCATCCTACA 57.194 30.769 0.00 0.00 0.00 2.74
63 64 8.892723 GGTGAGATCAATACAACACAATATTCA 58.107 33.333 0.00 0.00 0.00 2.57
64 65 9.113838 AGGTGAGATCAATACAACACAATATTC 57.886 33.333 0.00 0.00 0.00 1.75
70 71 9.546428 CATATTAGGTGAGATCAATACAACACA 57.454 33.333 0.00 0.00 0.00 3.72
71 72 8.993121 CCATATTAGGTGAGATCAATACAACAC 58.007 37.037 0.00 0.00 0.00 3.32
72 73 8.156820 CCCATATTAGGTGAGATCAATACAACA 58.843 37.037 0.00 0.00 0.00 3.33
73 74 7.607991 CCCCATATTAGGTGAGATCAATACAAC 59.392 40.741 0.00 0.00 0.00 3.32
74 75 7.294720 ACCCCATATTAGGTGAGATCAATACAA 59.705 37.037 0.00 0.00 34.20 2.41
75 76 6.792473 ACCCCATATTAGGTGAGATCAATACA 59.208 38.462 0.00 0.00 34.20 2.29
76 77 7.259088 ACCCCATATTAGGTGAGATCAATAC 57.741 40.000 0.00 0.00 34.20 1.89
78 79 9.749996 ATATACCCCATATTAGGTGAGATCAAT 57.250 33.333 4.01 0.00 36.88 2.57
95 96 9.883293 CCTCTCATGTATTCTATATATACCCCA 57.117 37.037 0.00 0.00 0.00 4.96
103 104 9.586732 GCCTCTATCCTCTCATGTATTCTATAT 57.413 37.037 0.00 0.00 0.00 0.86
104 105 8.786838 AGCCTCTATCCTCTCATGTATTCTATA 58.213 37.037 0.00 0.00 0.00 1.31
105 106 7.651607 AGCCTCTATCCTCTCATGTATTCTAT 58.348 38.462 0.00 0.00 0.00 1.98
106 107 7.038531 AGCCTCTATCCTCTCATGTATTCTA 57.961 40.000 0.00 0.00 0.00 2.10
107 108 5.902760 AGCCTCTATCCTCTCATGTATTCT 58.097 41.667 0.00 0.00 0.00 2.40
108 109 6.210385 TCAAGCCTCTATCCTCTCATGTATTC 59.790 42.308 0.00 0.00 0.00 1.75
109 110 6.080682 TCAAGCCTCTATCCTCTCATGTATT 58.919 40.000 0.00 0.00 0.00 1.89
110 111 5.649265 TCAAGCCTCTATCCTCTCATGTAT 58.351 41.667 0.00 0.00 0.00 2.29
111 112 5.066913 TCAAGCCTCTATCCTCTCATGTA 57.933 43.478 0.00 0.00 0.00 2.29
112 113 3.921104 TCAAGCCTCTATCCTCTCATGT 58.079 45.455 0.00 0.00 0.00 3.21
113 114 4.344679 ACTTCAAGCCTCTATCCTCTCATG 59.655 45.833 0.00 0.00 0.00 3.07
114 115 4.555689 ACTTCAAGCCTCTATCCTCTCAT 58.444 43.478 0.00 0.00 0.00 2.90
115 116 3.987745 ACTTCAAGCCTCTATCCTCTCA 58.012 45.455 0.00 0.00 0.00 3.27
116 117 4.890581 TGTACTTCAAGCCTCTATCCTCTC 59.109 45.833 0.00 0.00 0.00 3.20
117 118 4.873010 TGTACTTCAAGCCTCTATCCTCT 58.127 43.478 0.00 0.00 0.00 3.69
118 119 5.596845 CTTGTACTTCAAGCCTCTATCCTC 58.403 45.833 0.00 0.00 45.37 3.71
119 120 5.606348 CTTGTACTTCAAGCCTCTATCCT 57.394 43.478 0.00 0.00 45.37 3.24
130 131 9.214957 CCATGTATTACTTGTCTTGTACTTCAA 57.785 33.333 8.42 0.00 34.61 2.69
131 132 8.372459 ACCATGTATTACTTGTCTTGTACTTCA 58.628 33.333 8.42 0.00 0.00 3.02
132 133 8.773404 ACCATGTATTACTTGTCTTGTACTTC 57.227 34.615 8.42 0.00 0.00 3.01
133 134 9.569122 AAACCATGTATTACTTGTCTTGTACTT 57.431 29.630 8.42 0.00 0.00 2.24
156 157 8.706521 AGGAGTAGAGATGGAATAGGTTTAAAC 58.293 37.037 9.98 9.98 0.00 2.01
157 158 8.855804 AGGAGTAGAGATGGAATAGGTTTAAA 57.144 34.615 0.00 0.00 0.00 1.52
158 159 8.855804 AAGGAGTAGAGATGGAATAGGTTTAA 57.144 34.615 0.00 0.00 0.00 1.52
160 161 9.095700 GATAAGGAGTAGAGATGGAATAGGTTT 57.904 37.037 0.00 0.00 0.00 3.27
161 162 8.461033 AGATAAGGAGTAGAGATGGAATAGGTT 58.539 37.037 0.00 0.00 0.00 3.50
162 163 8.006967 AGATAAGGAGTAGAGATGGAATAGGT 57.993 38.462 0.00 0.00 0.00 3.08
163 164 8.336235 AGAGATAAGGAGTAGAGATGGAATAGG 58.664 40.741 0.00 0.00 0.00 2.57
393 395 9.330063 AGGAACAACACTTGTATATGTCATATG 57.670 33.333 14.54 0.00 44.59 1.78
399 401 8.135382 AGACTAGGAACAACACTTGTATATGT 57.865 34.615 0.00 0.00 44.59 2.29
410 412 4.202223 GGTTGTGAGAGACTAGGAACAACA 60.202 45.833 15.80 5.23 45.70 3.33
436 438 9.099454 CCAATCTAGTTATGAGGTGAGTTTAAC 57.901 37.037 0.00 0.00 0.00 2.01
484 487 5.046529 CGACCAACACCATCAATTCAAAAA 58.953 37.500 0.00 0.00 0.00 1.94
485 488 4.500545 CCGACCAACACCATCAATTCAAAA 60.501 41.667 0.00 0.00 0.00 2.44
541 545 9.472361 ACTCACATTTTCTTTCAATCATTTGAG 57.528 29.630 0.00 0.00 42.60 3.02
776 943 8.635765 TGCCATTAATTTCCCTAAGATATGAC 57.364 34.615 0.00 0.00 0.00 3.06
930 1127 0.313987 TATGCATCTGAGCGTACCGG 59.686 55.000 0.19 0.00 37.31 5.28
972 1169 4.415881 AACCTGGAATTGTTGGTTTTCC 57.584 40.909 0.00 0.00 39.48 3.13
1102 1299 5.280499 TCCTTGATAAGTGAGAATCTGGGA 58.720 41.667 0.00 0.00 34.92 4.37
1286 1483 4.407365 ACCTGGGTTTTATGGTCTTTCAG 58.593 43.478 0.00 0.00 0.00 3.02
1335 1532 6.754702 ATATAGTGAGCAATTCATGGATGC 57.245 37.500 9.39 9.39 38.29 3.91
1477 1692 8.514330 ACTATGTCAAAAGGTTGTTACTTCAA 57.486 30.769 0.00 0.00 36.07 2.69
1534 1749 7.645340 GGATCAGACAATACATACAAAACATGC 59.355 37.037 0.00 0.00 0.00 4.06
1721 1938 5.950544 ATGGTGCTACTTCCATTACTACA 57.049 39.130 0.00 0.00 41.02 2.74
1783 2000 6.002082 ACTTATACAAAAACTCACCTCCCAC 58.998 40.000 0.00 0.00 0.00 4.61
2003 2226 3.694566 ACCCTCGATGGAAAATTAACTGC 59.305 43.478 14.21 0.00 38.35 4.40
2185 2477 9.345517 CCTTCATGTACAACTGAAATAATGTTG 57.654 33.333 11.89 0.00 44.44 3.33
2319 2617 5.529581 TTCACATTTTGGGAAGGAAAGAC 57.470 39.130 0.00 0.00 34.34 3.01
2344 2642 5.886960 ACTTCAATCTTAAGATGTGTGGC 57.113 39.130 18.61 0.00 34.49 5.01
2459 2773 9.036671 CCACTAATTAAGCTAAGAAGTTCTAGC 57.963 37.037 18.82 18.82 35.91 3.42
2539 2853 9.950496 GATAAACCTGATAGGATATCACATGTT 57.050 33.333 4.83 5.87 37.67 2.71
2584 3009 2.695359 AGTAACGTCCGCAAATGTGAT 58.305 42.857 0.00 0.00 0.00 3.06
2595 3020 5.049680 TCTGCAAGAAATCAAAGTAACGTCC 60.050 40.000 0.00 0.00 42.31 4.79
2598 3023 5.385617 CCTCTGCAAGAAATCAAAGTAACG 58.614 41.667 0.00 0.00 46.34 3.18
2607 3032 1.379642 CCCGCCCTCTGCAAGAAATC 61.380 60.000 0.00 0.00 46.34 2.17
2637 3062 2.887337 CGCCCCAAATAAATCACCAAC 58.113 47.619 0.00 0.00 0.00 3.77
2692 3118 4.157849 GCTAGAATCCTGGCTACCTTTT 57.842 45.455 0.00 0.00 42.77 2.27
2746 3172 0.729116 CCATCCGATCTGTGTGTTGC 59.271 55.000 0.00 0.00 0.00 4.17
2850 3285 9.466497 CCAATAATAGCCTGTATGTATCCAAAT 57.534 33.333 0.00 0.00 0.00 2.32
2851 3286 7.393234 GCCAATAATAGCCTGTATGTATCCAAA 59.607 37.037 0.00 0.00 0.00 3.28
2852 3287 6.884295 GCCAATAATAGCCTGTATGTATCCAA 59.116 38.462 0.00 0.00 0.00 3.53
2853 3288 6.215431 AGCCAATAATAGCCTGTATGTATCCA 59.785 38.462 0.00 0.00 0.00 3.41
2854 3289 6.653989 AGCCAATAATAGCCTGTATGTATCC 58.346 40.000 0.00 0.00 0.00 2.59
2865 3300 9.903682 CATGCAAATATATAGCCAATAATAGCC 57.096 33.333 0.00 0.00 0.00 3.93
2924 3413 4.006319 TGTTCCAAGGCCAAAAACAAAAG 58.994 39.130 5.01 0.00 0.00 2.27
2965 3454 5.927030 TCAACGCATGACTTCTTTGAATAC 58.073 37.500 0.00 0.00 31.50 1.89
3010 3499 1.374560 CAACGTTGTGGTGGACTTGA 58.625 50.000 20.21 0.00 0.00 3.02
3106 3595 9.722056 AATCGCAGATTTTAAGAATGACATAAC 57.278 29.630 0.00 0.00 45.12 1.89
3125 3618 1.446907 AGGTGCTTGAGAAATCGCAG 58.553 50.000 0.00 0.00 32.38 5.18
3209 3711 6.464222 CCTGATGTCGGCTCCTAAAATAATA 58.536 40.000 0.00 0.00 0.00 0.98
3210 3712 5.308825 CCTGATGTCGGCTCCTAAAATAAT 58.691 41.667 0.00 0.00 0.00 1.28
3314 3816 2.050442 CGCCCCAGAACGCAAAAC 60.050 61.111 0.00 0.00 0.00 2.43
3370 3872 0.179018 AAATGCCCGCTACCCATCTC 60.179 55.000 0.00 0.00 0.00 2.75
3395 3897 1.448985 CGCTTTTCCGAATCCTTCCA 58.551 50.000 0.00 0.00 0.00 3.53
3441 3943 4.035208 GTCACAAACCAGCCCTTATTATCG 59.965 45.833 0.00 0.00 0.00 2.92
3554 4056 3.010138 CCCTGGTCCACCATAGAAGAAAA 59.990 47.826 0.00 0.00 46.46 2.29
3556 4058 2.196595 CCCTGGTCCACCATAGAAGAA 58.803 52.381 0.00 0.00 46.46 2.52
3668 4187 3.724128 CGGAAGTCGATGATATACGGACG 60.724 52.174 0.00 0.00 42.43 4.79
3849 6211 3.368013 CCGCCACAAGTACAGATCTGTTA 60.368 47.826 32.14 15.77 41.83 2.41
3854 6216 1.204941 AGTCCGCCACAAGTACAGATC 59.795 52.381 0.00 0.00 0.00 2.75
3858 6220 3.472283 TTTTAGTCCGCCACAAGTACA 57.528 42.857 0.00 0.00 0.00 2.90
3859 6221 4.060205 TCTTTTTAGTCCGCCACAAGTAC 58.940 43.478 0.00 0.00 0.00 2.73
3860 6222 4.339872 TCTTTTTAGTCCGCCACAAGTA 57.660 40.909 0.00 0.00 0.00 2.24
3861 6223 3.202829 TCTTTTTAGTCCGCCACAAGT 57.797 42.857 0.00 0.00 0.00 3.16
3863 6225 3.242804 CGTTTCTTTTTAGTCCGCCACAA 60.243 43.478 0.00 0.00 0.00 3.33
3864 6226 2.288458 CGTTTCTTTTTAGTCCGCCACA 59.712 45.455 0.00 0.00 0.00 4.17
3865 6227 2.350102 CCGTTTCTTTTTAGTCCGCCAC 60.350 50.000 0.00 0.00 0.00 5.01
3866 6228 1.874872 CCGTTTCTTTTTAGTCCGCCA 59.125 47.619 0.00 0.00 0.00 5.69
3868 6230 2.159037 CCTCCGTTTCTTTTTAGTCCGC 59.841 50.000 0.00 0.00 0.00 5.54
3869 6231 2.740447 CCCTCCGTTTCTTTTTAGTCCG 59.260 50.000 0.00 0.00 0.00 4.79
3870 6232 4.001652 CTCCCTCCGTTTCTTTTTAGTCC 58.998 47.826 0.00 0.00 0.00 3.85
3871 6233 4.639334 ACTCCCTCCGTTTCTTTTTAGTC 58.361 43.478 0.00 0.00 0.00 2.59
3872 6234 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
3873 6235 8.782339 TTATTACTCCCTCCGTTTCTTTTTAG 57.218 34.615 0.00 0.00 0.00 1.85
3875 6237 9.743581 TTATTATTACTCCCTCCGTTTCTTTTT 57.256 29.630 0.00 0.00 0.00 1.94
3876 6238 9.170734 GTTATTATTACTCCCTCCGTTTCTTTT 57.829 33.333 0.00 0.00 0.00 2.27
3877 6239 8.323567 TGTTATTATTACTCCCTCCGTTTCTTT 58.676 33.333 0.00 0.00 0.00 2.52
3878 6240 7.854337 TGTTATTATTACTCCCTCCGTTTCTT 58.146 34.615 0.00 0.00 0.00 2.52
3879 6241 7.427989 TGTTATTATTACTCCCTCCGTTTCT 57.572 36.000 0.00 0.00 0.00 2.52
3880 6242 8.496707 TTTGTTATTATTACTCCCTCCGTTTC 57.503 34.615 0.00 0.00 0.00 2.78
3881 6243 8.899771 CATTTGTTATTATTACTCCCTCCGTTT 58.100 33.333 0.00 0.00 0.00 3.60
3882 6244 8.269317 TCATTTGTTATTATTACTCCCTCCGTT 58.731 33.333 0.00 0.00 0.00 4.44
3883 6245 7.713942 GTCATTTGTTATTATTACTCCCTCCGT 59.286 37.037 0.00 0.00 0.00 4.69
3884 6246 7.713507 TGTCATTTGTTATTATTACTCCCTCCG 59.286 37.037 0.00 0.00 0.00 4.63
3885 6247 8.974060 TGTCATTTGTTATTATTACTCCCTCC 57.026 34.615 0.00 0.00 0.00 4.30
3938 7003 3.288092 TCATCGTGTCACCATAGCTACT 58.712 45.455 0.00 0.00 0.00 2.57
3939 7004 3.315470 TCTCATCGTGTCACCATAGCTAC 59.685 47.826 0.00 0.00 0.00 3.58
3942 7007 2.871182 TCTCATCGTGTCACCATAGC 57.129 50.000 0.00 0.00 0.00 2.97
3943 7008 4.936891 TCATTCTCATCGTGTCACCATAG 58.063 43.478 0.00 0.00 0.00 2.23
3945 7010 3.448660 TCTCATTCTCATCGTGTCACCAT 59.551 43.478 0.00 0.00 0.00 3.55
3947 7012 3.182967 GTCTCATTCTCATCGTGTCACC 58.817 50.000 0.00 0.00 0.00 4.02
3948 7013 3.182967 GGTCTCATTCTCATCGTGTCAC 58.817 50.000 0.00 0.00 0.00 3.67
3949 7014 2.825532 TGGTCTCATTCTCATCGTGTCA 59.174 45.455 0.00 0.00 0.00 3.58
3954 7019 1.405463 TCGGTGGTCTCATTCTCATCG 59.595 52.381 0.00 0.00 35.35 3.84
3956 7021 3.515502 TCTTTCGGTGGTCTCATTCTCAT 59.484 43.478 0.00 0.00 0.00 2.90
3958 7023 3.254892 GTCTTTCGGTGGTCTCATTCTC 58.745 50.000 0.00 0.00 0.00 2.87
4167 7232 2.358003 GCACGAGCTCCTGCAGTT 60.358 61.111 26.54 0.00 42.74 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.